The present invention relates to drug screening, and more particularly, to analysis of protein binding reactions using a nanochannel-based chip.
In the fields of medicine, biotechnology, and pharmacology, drug discovery is the process by which new candidate medications are discovered. Historically, drugs were discovered through identifying the active ingredient from traditional remedies or by serendipitous discovery. Later, chemical libraries of synthetic small molecules, natural products, or extracts were screened in intact cells or whole organisms to identify substances that have a desirable therapeutic effect in a process known as classical pharmacology. Since sequencing of the human genome, which allowed rapid cloning and synthesis of large quantities of purified proteins, it has become common practice to use throughput screening of large compound libraries against isolated biological targets which are hypothesized to be disease modifying in a process known as reverse pharmacology. Hits from these screens are then tested in cells and then in animals for efficacy. Even more recently, scientists have been able to understand the shape of biological molecules at the atomic level, and to use that knowledge to design drug candidates (i.e., drug design).
Modern drug discovery involves the identification of screening hits, medicinal chemistry optimization of those hits to increase the affinity, selectivity (to reduce the potential of side effects), efficacy/potency, metabolic stability (to increase the half-life), and oral bioavailability. Once a compound that fulfills all of these requirements has been identified, it will begin the process of drug development prior to clinical trials.
Despite advances in technology and understanding of biological systems, drug discovery is still a lengthy, expensive, difficult, and inefficient process with a low rate of new therapeutic discovery. It is recognized that the research and development cost of each new molecular entity (NME) is approximately $1.8 billion (US).
With regard to drug targets, the definition of “target” itself is something argued within the pharmaceutical industry. Generally, the target is the naturally existing cellular or molecular structure involved in the pathology of interest that the drug-in-development is meant to act on. However, the distinction between a new and established target can be made without a full understanding of just what a target is. This distinction is typically made by pharmaceutical companies engaged in discovery and development of therapeutics. “Established targets” are those for which there is a good scientific understanding, supported by a lengthy publication history, of both how the target functions in normal physiology and how it is involved in human pathology. This does not imply that the mechanism of action of drugs that are thought to act through a particular established target is fully understood. Rather, “established” relates directly to the amount of background information available on a target, in particular functional information. The more such information is available, the less investment is (generally) required to develop a therapeutic directed against the target. The process of gathering such functional information is called “target validation” in pharmaceutical industry parlance. Established targets also include those that the pharmaceutical industry has had experience mounting drug discovery campaigns against in the past; such a history provides information on the chemical feasibility of developing a small molecular therapeutic against the target and can provide licensing opportunities and freedom-to-operate indicators with respect to small-molecule therapeutic candidates.
In general, “new targets” are all those targets that are not “established targets” but which have been or are the subject of drug discovery campaigns. These typically include newly discovered proteins, or proteins whose function has now become clear as a result of basic scientific research. The majority of targets currently selected for drug discovery efforts are proteins. Two classes predominate: G protein coupled receptors (or GPCRs) and protein kinases.
The process of finding a new drug against a chosen target for a particular disease usually involves high-throughput screening (HTS), wherein large libraries of chemicals are tested for their ability to modify the target. For example, if the target is a novel GPCR, compounds will be screened for their ability to inhibit or stimulate that receptor in cells (e.g., antagonist and agonist): if the target is a protein kinase, the chemicals will be tested for their ability to inhibit that kinase. Furthermore, fragment-based lead discovery (FBLD), sometimes referred to as fragment-based drug discovery (FBDD), is used to identify lead compounds as part of the drug discovery process. The aspect involves the identification of small chemical fragments, which can bind, sometimes only weakly, to the biological target, and then can be grown or combined to produce a lead with a higher affinity. As a result of the FBLD process, libraries with a few thousand compounds with molecular weights of about 200 Da can be screened, and millimolar affinities can be employed.